Miles Trochesset

Department of Computer Science  
University of Toronto

In September 2004 I finished a M.Sc. in the Database Group of the Department of Computer Science at the University of Toronto, although most of my work was with the Machine Learning Group. I started this M.Sc. in September 2002 under the supervision of Anthony Bonner. My master's thesis dealt with data mining and pattern recognition in a particular case of datasets with very few positive samples. I worked on a bioinformatics application: statistical learning of gene annotations in Saccharomyces cerevisiae.

From September 2003 to February 2005, I was also working in Hughes' Lab at the Best Institute doing analysis and processing of biological data. My main activities were database development, statistical analysis, and software development.

Research, Publications & Projects

  • Detection and discovery of RNA modifications using microarrays.
    Shawna L. Hiley, Jane Jackman, Tomas Babak, Miles Trochesset, Quaid D. Morris, Eric Phizicky, and Timothy R. Hughes
    Nucleic Acids Research 2005 Jan 7;33(1):e2
    HTML - PDF

  • Statistical Learning of Gene Annotations in Saccharomyces Cerevisiae
    M.Sc. Thesis, Department of Computer Science, University of Toronto. Sept 2004.
    PDF - PS

  • Clustering Labeled Data and Cross-Validation for Classification with Few Positives in Yeast
    Miles Trochesset and Anthony Bonner.
    In Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD) at KDD 2004, Seattle, WA, USA, August 22-25, 2004.
    PDF - PS

  • Exploration of Essential Gene Functions Via Titratable Promoter Alleles
    Cell 2004 July 9;118(1):31-44.

  • A Global View of Yeast Noncoding RNA, Processing and Modification
    Shawna Hiley, Miles Trochesset, Quaid Morris, Tomas Babak and Tim Hughes
    RNA 2004 (9th Annual Meeting of the RNA Society), University of Wisconsin, Madison, June 1-6 2004.
    Yeast 2004 (Yeast Genetics and Molecular Biology Meeting), University of Washington, Seattle, July 27 - August 1st 2004.

  • Microarray analysis and normalization.
    Statistical techniques, software development for custom arrays.

  • Design of 60-mer oligonucleotides for whole-genome analysis of Fugu Rubripes, Tetraodon, Saccharomyces cerevisiae, Mus musculus, Gallus gallus and Xenopus tropicalis.

  • Building a non redundant list of all known and predicted Mouse genes.
    Work done in common with Mark Robinson.
    Involves querying MGI, GenBank, RefSeq, Novartis, EnsEMBL, UniGene, GeneID etc. and mapping all hits to the Mouse chromosomes (Build 32) to detect redundancy.

Teaching Assistantships

Miles Trochesset, Database Group, UofT Dept. of Computer Science ||
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